Multiple sequence alignment - TraesCS3A01G320900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G320900 chr3A 100.000 3088 0 0 1 3088 564347735 564344648 0.000000e+00 5703.0
1 TraesCS3A01G320900 chr3D 90.283 1626 117 21 726 2342 424655118 424656711 0.000000e+00 2089.0
2 TraesCS3A01G320900 chr3D 89.799 696 48 6 1 683 424653256 424653941 0.000000e+00 870.0
3 TraesCS3A01G320900 chr3D 94.758 496 20 3 2597 3088 424656989 424657482 0.000000e+00 767.0
4 TraesCS3A01G320900 chr3B 89.615 1560 126 22 737 2271 554648195 554649743 0.000000e+00 1951.0
5 TraesCS3A01G320900 chr3B 89.755 654 36 12 60 682 554647408 554648061 0.000000e+00 808.0
6 TraesCS3A01G320900 chr3B 93.131 495 26 5 2597 3088 554697251 554697740 0.000000e+00 719.0
7 TraesCS3A01G320900 chr6D 87.408 1501 138 31 807 2270 457010358 457011844 0.000000e+00 1677.0
8 TraesCS3A01G320900 chr6D 87.660 470 27 6 2597 3060 457064944 457065388 4.560000e-143 518.0
9 TraesCS3A01G320900 chr6D 93.478 46 3 0 3043 3088 457065467 457065512 5.530000e-08 69.4
10 TraesCS3A01G320900 chr5D 90.312 1280 101 11 999 2276 547262167 547260909 0.000000e+00 1655.0
11 TraesCS3A01G320900 chr5D 95.094 265 10 2 2825 3088 547260837 547260575 6.160000e-112 414.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G320900 chr3A 564344648 564347735 3087 True 5703.0 5703 100.000000 1 3088 1 chr3A.!!$R1 3087
1 TraesCS3A01G320900 chr3D 424653256 424657482 4226 False 1242.0 2089 91.613333 1 3088 3 chr3D.!!$F1 3087
2 TraesCS3A01G320900 chr3B 554647408 554649743 2335 False 1379.5 1951 89.685000 60 2271 2 chr3B.!!$F2 2211
3 TraesCS3A01G320900 chr6D 457010358 457011844 1486 False 1677.0 1677 87.408000 807 2270 1 chr6D.!!$F1 1463
4 TraesCS3A01G320900 chr6D 457064944 457065512 568 False 293.7 518 90.569000 2597 3088 2 chr6D.!!$F2 491
5 TraesCS3A01G320900 chr5D 547260575 547262167 1592 True 1034.5 1655 92.703000 999 3088 2 chr5D.!!$R1 2089

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
47 48 0.112995 AGGGAGGCAAACATGCAGAA 59.887 50.0 2.97 0.00 36.33 3.02 F
1829 3085 0.164647 AACTTCTACGACGGTCGACG 59.835 55.0 34.40 23.17 43.74 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 3265 0.318441 CCTTCTCGTCACCTGCAGAA 59.682 55.0 17.39 0.00 0.00 3.02 R
3004 4389 0.171007 CAAGTAAGGCGCAACCATGG 59.829 55.0 11.19 11.19 43.14 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.055891 ACAAAATAGGGAGGCAAACATGC 60.056 43.478 0.00 0.00 0.00 4.06
44 45 2.530460 AATAGGGAGGCAAACATGCA 57.470 45.000 2.97 0.00 36.33 3.96
45 46 2.062971 ATAGGGAGGCAAACATGCAG 57.937 50.000 2.97 0.00 36.33 4.41
46 47 0.991146 TAGGGAGGCAAACATGCAGA 59.009 50.000 2.97 0.00 36.33 4.26
47 48 0.112995 AGGGAGGCAAACATGCAGAA 59.887 50.000 2.97 0.00 36.33 3.02
48 49 0.968405 GGGAGGCAAACATGCAGAAA 59.032 50.000 2.97 0.00 36.33 2.52
49 50 1.337167 GGGAGGCAAACATGCAGAAAC 60.337 52.381 2.97 0.00 36.33 2.78
50 51 1.340889 GGAGGCAAACATGCAGAAACA 59.659 47.619 2.97 0.00 36.33 2.83
80 81 0.523072 CCATGTTCCGCTGTCCAAAG 59.477 55.000 0.00 0.00 0.00 2.77
103 104 1.003355 CCCAGAAGCGCCTTGAAGA 60.003 57.895 2.29 0.00 0.00 2.87
438 468 1.471153 GGAGACGAAAGGGGAACGATC 60.471 57.143 0.00 0.00 0.00 3.69
443 473 2.094130 ACGAAAGGGGAACGATCTCTTC 60.094 50.000 0.00 0.00 0.00 2.87
491 521 3.564053 TTCACGGTGGGAAACTAAAGT 57.436 42.857 8.50 0.00 0.00 2.66
546 585 5.273170 TCAGAGAATGTTTCGCTTTTGTTG 58.727 37.500 0.00 0.00 37.74 3.33
569 622 1.676006 CCGCTTTCTTTCACCTGTTGT 59.324 47.619 0.00 0.00 0.00 3.32
578 631 1.596603 TCACCTGTTGTGTGCATCAG 58.403 50.000 0.00 0.00 45.61 2.90
579 632 1.140652 TCACCTGTTGTGTGCATCAGA 59.859 47.619 0.00 0.00 45.61 3.27
584 637 7.765304 CACCTGTTGTGTGCATCAGAATGAC 62.765 48.000 0.00 0.00 44.23 3.06
611 664 1.000486 GGAGGCCTTCCCCTTTTCC 60.000 63.158 6.77 0.00 40.37 3.13
687 740 1.670811 GACAACTTGGTGGCCATATCG 59.329 52.381 9.72 0.45 31.53 2.92
688 741 1.280710 ACAACTTGGTGGCCATATCGA 59.719 47.619 9.72 0.70 31.53 3.59
689 742 2.092429 ACAACTTGGTGGCCATATCGAT 60.092 45.455 9.72 2.16 31.53 3.59
691 744 4.202461 ACAACTTGGTGGCCATATCGATAT 60.202 41.667 9.72 12.25 31.53 1.63
692 745 3.942829 ACTTGGTGGCCATATCGATATG 58.057 45.455 30.41 30.41 39.80 1.78
719 1358 4.066646 TCGATGGTGTTTTGTTCTCAGA 57.933 40.909 0.00 0.00 0.00 3.27
742 1929 0.311790 CATATTCCACACATGCGGGC 59.688 55.000 0.00 0.00 0.00 6.13
801 2001 4.294523 CGGCTTCCATCCGTTGAA 57.705 55.556 0.00 0.00 41.85 2.69
811 2011 2.419990 CCATCCGTTGAAGCACTGGATA 60.420 50.000 0.00 0.00 37.33 2.59
844 2048 7.331687 CCATTAAACAATAGCAGTTCCTTTTGG 59.668 37.037 0.00 0.00 42.21 3.28
910 2118 7.094162 TGACCACATTAACAAGACTCAACAAAA 60.094 33.333 0.00 0.00 0.00 2.44
928 2136 0.379316 AACGTTCGTTTGTTGCTCCC 59.621 50.000 4.72 0.00 0.00 4.30
930 2138 0.378962 CGTTCGTTTGTTGCTCCCAA 59.621 50.000 0.00 0.00 0.00 4.12
938 2146 1.300620 GTTGCTCCCAAAAACCGCC 60.301 57.895 0.00 0.00 31.68 6.13
941 2149 3.047735 CTCCCAAAAACCGCCACC 58.952 61.111 0.00 0.00 0.00 4.61
942 2150 1.530655 CTCCCAAAAACCGCCACCT 60.531 57.895 0.00 0.00 0.00 4.00
966 2201 9.045223 CCTTCCTTTAAAATGGTTTGAAAGAAG 57.955 33.333 11.94 12.00 38.87 2.85
974 2209 8.822652 AAAATGGTTTGAAAGAAGCTCATTAG 57.177 30.769 0.00 0.00 0.00 1.73
975 2210 7.530426 AATGGTTTGAAAGAAGCTCATTAGT 57.470 32.000 0.00 0.00 0.00 2.24
977 2212 5.827797 TGGTTTGAAAGAAGCTCATTAGTGT 59.172 36.000 0.00 0.00 0.00 3.55
978 2213 6.017109 TGGTTTGAAAGAAGCTCATTAGTGTC 60.017 38.462 0.00 0.00 0.00 3.67
979 2214 6.017109 GGTTTGAAAGAAGCTCATTAGTGTCA 60.017 38.462 0.00 0.00 0.00 3.58
980 2215 7.417612 GTTTGAAAGAAGCTCATTAGTGTCAA 58.582 34.615 0.00 0.00 0.00 3.18
982 2217 8.846943 TTGAAAGAAGCTCATTAGTGTCAATA 57.153 30.769 0.00 0.00 0.00 1.90
983 2218 8.484641 TGAAAGAAGCTCATTAGTGTCAATAG 57.515 34.615 0.00 0.00 0.00 1.73
984 2219 8.314021 TGAAAGAAGCTCATTAGTGTCAATAGA 58.686 33.333 0.00 0.00 0.00 1.98
1011 2267 2.076100 CGTCTAAGCATGGCACTCAAA 58.924 47.619 0.00 0.00 0.00 2.69
1183 2439 1.377202 GGGAAGATGCGGCAGAACA 60.377 57.895 9.25 0.00 0.00 3.18
1194 2450 4.680237 CAGAACAGCGGCCACGGA 62.680 66.667 2.24 0.00 41.36 4.69
1359 2615 2.051879 TCTTCGTCAAGAGCTTCACG 57.948 50.000 0.00 0.00 33.38 4.35
1824 3080 2.735823 GTCAACAACTTCTACGACGGT 58.264 47.619 0.00 0.00 0.00 4.83
1825 3081 2.723143 GTCAACAACTTCTACGACGGTC 59.277 50.000 0.00 0.00 0.00 4.79
1826 3082 1.712350 CAACAACTTCTACGACGGTCG 59.288 52.381 27.33 27.33 46.93 4.79
1827 3083 1.229428 ACAACTTCTACGACGGTCGA 58.771 50.000 34.40 17.78 43.74 4.20
1828 3084 1.069636 ACAACTTCTACGACGGTCGAC 60.070 52.381 34.40 7.13 43.74 4.20
1829 3085 0.164647 AACTTCTACGACGGTCGACG 59.835 55.000 34.40 23.17 43.74 5.12
1840 3096 3.450115 GTCGACGGGTGGAGGGAG 61.450 72.222 0.00 0.00 0.00 4.30
1888 3144 0.323178 CTGTCAAGAGCCAGGGCAAT 60.323 55.000 13.63 0.00 44.88 3.56
1988 3247 1.746615 GAATTGCCAGAGCTCGCCA 60.747 57.895 8.37 3.96 40.80 5.69
1990 3249 1.381928 AATTGCCAGAGCTCGCCATG 61.382 55.000 8.37 0.38 40.80 3.66
2006 3265 5.620206 TCGCCATGTGATCTTGGTATATTT 58.380 37.500 10.35 0.00 39.93 1.40
2008 3267 6.204688 TCGCCATGTGATCTTGGTATATTTTC 59.795 38.462 10.35 0.00 39.93 2.29
2149 3411 3.270027 CCGAATTACAACAGGCATCAGA 58.730 45.455 0.00 0.00 0.00 3.27
2258 3521 3.128938 ACGGAGAGAATAAAGACGTCCAG 59.871 47.826 13.01 0.00 0.00 3.86
2263 3526 4.527038 AGAGAATAAAGACGTCCAGTGGAA 59.473 41.667 15.09 0.00 31.38 3.53
2264 3527 5.011738 AGAGAATAAAGACGTCCAGTGGAAA 59.988 40.000 15.09 0.00 31.38 3.13
2271 3534 3.133362 AGACGTCCAGTGGAAAGTGTTAA 59.867 43.478 22.00 0.00 31.38 2.01
2272 3535 4.062991 GACGTCCAGTGGAAAGTGTTAAT 58.937 43.478 22.00 1.22 31.38 1.40
2273 3536 5.011329 AGACGTCCAGTGGAAAGTGTTAATA 59.989 40.000 22.00 0.00 31.38 0.98
2274 3537 4.992951 ACGTCCAGTGGAAAGTGTTAATAC 59.007 41.667 15.09 0.00 31.38 1.89
2328 3620 5.523369 GCTTGTAGCTATAAAAATGGCTGG 58.477 41.667 4.38 0.00 38.82 4.85
2330 3622 4.469657 TGTAGCTATAAAAATGGCTGGGG 58.530 43.478 6.50 0.00 38.82 4.96
2338 3630 4.617253 AAAAATGGCTGGGGTTTTACTC 57.383 40.909 0.00 0.00 0.00 2.59
2342 3634 0.034380 GGCTGGGGTTTTACTCCCTC 60.034 60.000 0.00 0.00 38.22 4.30
2343 3635 0.034380 GCTGGGGTTTTACTCCCTCC 60.034 60.000 0.00 0.00 38.22 4.30
2349 3665 1.538512 GGTTTTACTCCCTCCGTTTGC 59.461 52.381 0.00 0.00 0.00 3.68
2358 3674 1.291877 CCTCCGTTTGCCTCAAGTCG 61.292 60.000 0.00 0.00 0.00 4.18
2367 3683 6.185399 CGTTTGCCTCAAGTCGAATTTATAG 58.815 40.000 0.00 0.00 0.00 1.31
2368 3684 6.487103 GTTTGCCTCAAGTCGAATTTATAGG 58.513 40.000 11.97 11.97 0.00 2.57
2375 3691 7.499232 CCTCAAGTCGAATTTATAGGGTTTGAT 59.501 37.037 0.00 0.00 0.00 2.57
2486 3819 9.810545 TTTGGATAAACTTTGTTAAACTTCAGG 57.189 29.630 0.00 0.00 0.00 3.86
2487 3820 8.754991 TGGATAAACTTTGTTAAACTTCAGGA 57.245 30.769 0.00 0.00 0.00 3.86
2488 3821 9.191479 TGGATAAACTTTGTTAAACTTCAGGAA 57.809 29.630 0.00 0.00 0.00 3.36
2489 3822 9.678941 GGATAAACTTTGTTAAACTTCAGGAAG 57.321 33.333 7.47 7.47 43.79 3.46
2502 3835 5.818136 CTTCAGGAAGTTGAGTTGAAACA 57.182 39.130 0.83 0.00 33.87 2.83
2503 3836 6.194796 CTTCAGGAAGTTGAGTTGAAACAA 57.805 37.500 0.83 0.00 33.87 2.83
2504 3837 6.773976 TTCAGGAAGTTGAGTTGAAACAAT 57.226 33.333 0.00 0.00 0.00 2.71
2505 3838 6.377327 TCAGGAAGTTGAGTTGAAACAATC 57.623 37.500 0.00 0.00 0.00 2.67
2506 3839 5.299279 TCAGGAAGTTGAGTTGAAACAATCC 59.701 40.000 0.00 0.00 36.66 3.01
2507 3840 5.067674 CAGGAAGTTGAGTTGAAACAATCCA 59.932 40.000 11.35 0.00 37.84 3.41
2508 3841 5.835280 AGGAAGTTGAGTTGAAACAATCCAT 59.165 36.000 11.35 0.00 37.84 3.41
2509 3842 5.922544 GGAAGTTGAGTTGAAACAATCCATG 59.077 40.000 0.00 0.00 36.53 3.66
2510 3843 4.874970 AGTTGAGTTGAAACAATCCATGC 58.125 39.130 0.00 0.00 0.00 4.06
2511 3844 4.341806 AGTTGAGTTGAAACAATCCATGCA 59.658 37.500 0.00 0.00 0.00 3.96
2512 3845 4.933505 TGAGTTGAAACAATCCATGCAA 57.066 36.364 0.00 0.00 0.00 4.08
2513 3846 5.273674 TGAGTTGAAACAATCCATGCAAA 57.726 34.783 0.00 0.00 0.00 3.68
2514 3847 5.291178 TGAGTTGAAACAATCCATGCAAAG 58.709 37.500 0.00 0.00 0.00 2.77
2515 3848 5.163426 TGAGTTGAAACAATCCATGCAAAGT 60.163 36.000 0.00 0.00 0.00 2.66
2516 3849 5.673514 AGTTGAAACAATCCATGCAAAGTT 58.326 33.333 0.00 0.00 0.00 2.66
2517 3850 6.114767 AGTTGAAACAATCCATGCAAAGTTT 58.885 32.000 0.00 0.00 32.48 2.66
2518 3851 6.598850 AGTTGAAACAATCCATGCAAAGTTTT 59.401 30.769 0.00 0.00 30.23 2.43
2519 3852 6.998968 TGAAACAATCCATGCAAAGTTTTT 57.001 29.167 0.00 0.00 30.23 1.94
2548 3881 4.713792 AGTATTTCCTAGCATCCCTTGG 57.286 45.455 0.00 0.00 37.74 3.61
2561 3894 1.073284 TCCCTTGGAAGCGCTTTTACT 59.927 47.619 25.84 0.00 0.00 2.24
2572 3905 2.533561 GCGCTTTTACTAACCGCTAACG 60.534 50.000 0.00 0.00 41.28 3.18
2573 3906 2.663119 CGCTTTTACTAACCGCTAACGT 59.337 45.455 0.00 0.00 37.70 3.99
2579 3912 3.146618 ACTAACCGCTAACGTGATCTG 57.853 47.619 0.00 0.00 37.70 2.90
2592 3925 2.288666 GTGATCTGGCCTTCGCATAAA 58.711 47.619 3.32 0.00 36.38 1.40
2594 3927 3.316308 GTGATCTGGCCTTCGCATAAATT 59.684 43.478 3.32 0.00 36.38 1.82
2595 3928 3.953612 TGATCTGGCCTTCGCATAAATTT 59.046 39.130 3.32 0.00 36.38 1.82
2605 3982 6.563422 CCTTCGCATAAATTTTGGATTCTCA 58.437 36.000 0.00 0.00 0.00 3.27
2609 3986 9.434420 TTCGCATAAATTTTGGATTCTCAAATT 57.566 25.926 0.00 2.44 36.63 1.82
2663 4040 1.663161 GCCTTTCTTTTTCTCGGTGCG 60.663 52.381 0.00 0.00 0.00 5.34
2682 4059 2.739932 GCGCTAGAAGAATGCTGAAGGA 60.740 50.000 0.00 0.00 0.00 3.36
2689 4066 2.636830 AGAATGCTGAAGGAATGGACG 58.363 47.619 0.00 0.00 0.00 4.79
2690 4067 2.026822 AGAATGCTGAAGGAATGGACGT 60.027 45.455 0.00 0.00 0.00 4.34
2706 4084 1.405821 GACGTAGAGACATCCAGTGGG 59.594 57.143 9.92 0.00 0.00 4.61
2821 4199 0.677731 AGAATACCGACGACCCGACA 60.678 55.000 0.00 0.00 0.00 4.35
2867 4251 5.120830 CCACTCTATCAAAGTACAACACTGC 59.879 44.000 0.00 0.00 37.63 4.40
2956 4340 0.307760 GGTGTTGTTTCCGCACTCTG 59.692 55.000 0.00 0.00 33.96 3.35
2957 4341 1.295792 GTGTTGTTTCCGCACTCTGA 58.704 50.000 0.00 0.00 0.00 3.27
2979 4363 0.339859 AGGGCACATGAGTCTAGGGA 59.660 55.000 0.00 0.00 0.00 4.20
3004 4389 6.357367 TGATAATAGCCCTTTCCTTTCTGAC 58.643 40.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.500684 ACATGGTAAGCTTGTATGTTTCTG 57.499 37.500 9.86 0.00 0.00 3.02
44 45 6.151144 GGAACATGGTAAGCTTGTATGTTTCT 59.849 38.462 25.23 13.13 40.78 2.52
45 46 6.322491 GGAACATGGTAAGCTTGTATGTTTC 58.678 40.000 25.23 22.25 40.78 2.78
46 47 5.106317 CGGAACATGGTAAGCTTGTATGTTT 60.106 40.000 25.23 15.91 40.78 2.83
47 48 4.394920 CGGAACATGGTAAGCTTGTATGTT 59.605 41.667 24.97 24.97 42.68 2.71
48 49 3.938963 CGGAACATGGTAAGCTTGTATGT 59.061 43.478 9.86 13.30 33.73 2.29
49 50 3.242739 GCGGAACATGGTAAGCTTGTATG 60.243 47.826 9.86 12.68 0.00 2.39
50 51 2.943033 GCGGAACATGGTAAGCTTGTAT 59.057 45.455 9.86 0.00 0.00 2.29
80 81 1.973812 AAGGCGCTTCTGGGCTTTC 60.974 57.895 7.64 0.00 45.47 2.62
103 104 2.291190 GTCGCCGTCTAAAGCTCTCTAT 59.709 50.000 0.00 0.00 0.00 1.98
438 468 1.998315 CAGCTGGTGTCAATCGAAGAG 59.002 52.381 5.57 0.00 43.63 2.85
546 585 2.126850 GGTGAAAGAAAGCGGCGC 60.127 61.111 26.86 26.86 0.00 6.53
593 646 1.000486 GGAAAAGGGGAAGGCCTCC 60.000 63.158 5.23 9.41 44.54 4.30
657 710 0.320374 CCAAGTTGTCCGAGCCAGTA 59.680 55.000 1.45 0.00 0.00 2.74
687 740 6.706270 ACAAAACACCATCGATACTCCATATC 59.294 38.462 0.00 0.00 36.99 1.63
688 741 6.591935 ACAAAACACCATCGATACTCCATAT 58.408 36.000 0.00 0.00 0.00 1.78
689 742 5.984725 ACAAAACACCATCGATACTCCATA 58.015 37.500 0.00 0.00 0.00 2.74
691 744 4.280436 ACAAAACACCATCGATACTCCA 57.720 40.909 0.00 0.00 0.00 3.86
692 745 4.935808 AGAACAAAACACCATCGATACTCC 59.064 41.667 0.00 0.00 0.00 3.85
693 746 5.637810 TGAGAACAAAACACCATCGATACTC 59.362 40.000 0.00 0.00 0.00 2.59
695 748 5.637810 TCTGAGAACAAAACACCATCGATAC 59.362 40.000 0.00 0.00 0.00 2.24
697 750 4.641396 TCTGAGAACAAAACACCATCGAT 58.359 39.130 0.00 0.00 0.00 3.59
698 751 4.066646 TCTGAGAACAAAACACCATCGA 57.933 40.909 0.00 0.00 0.00 3.59
699 752 4.273480 AGTTCTGAGAACAAAACACCATCG 59.727 41.667 25.45 0.00 30.28 3.84
700 753 5.296780 TGAGTTCTGAGAACAAAACACCATC 59.703 40.000 25.45 12.12 30.28 3.51
701 754 5.192927 TGAGTTCTGAGAACAAAACACCAT 58.807 37.500 25.45 3.00 30.28 3.55
703 756 5.757850 ATGAGTTCTGAGAACAAAACACC 57.242 39.130 25.45 7.39 30.28 4.16
742 1929 3.119291 GGTGAGATCATAGTGAAGTGCG 58.881 50.000 0.00 0.00 0.00 5.34
800 2000 1.837439 TGGAACCGATATCCAGTGCTT 59.163 47.619 0.00 0.00 41.98 3.91
801 2001 1.496060 TGGAACCGATATCCAGTGCT 58.504 50.000 0.00 0.00 41.98 4.40
811 2011 5.885912 ACTGCTATTGTTTAATGGAACCGAT 59.114 36.000 0.00 0.00 0.00 4.18
884 2089 5.432645 TGTTGAGTCTTGTTAATGTGGTCA 58.567 37.500 0.00 0.00 0.00 4.02
910 2118 0.745128 TGGGAGCAACAAACGAACGT 60.745 50.000 0.00 0.00 0.00 3.99
928 2136 0.750249 AAGGAAGGTGGCGGTTTTTG 59.250 50.000 0.00 0.00 0.00 2.44
930 2138 2.368311 TAAAGGAAGGTGGCGGTTTT 57.632 45.000 0.00 0.00 0.00 2.43
938 2146 7.984617 TCTTTCAAACCATTTTAAAGGAAGGTG 59.015 33.333 0.71 0.00 0.00 4.00
941 2149 8.551205 GCTTCTTTCAAACCATTTTAAAGGAAG 58.449 33.333 0.71 9.30 34.95 3.46
942 2150 8.264347 AGCTTCTTTCAAACCATTTTAAAGGAA 58.736 29.630 0.71 1.67 0.00 3.36
983 2218 2.412847 GCCATGCTTAGACGTGTTTGTC 60.413 50.000 0.00 0.00 39.21 3.18
984 2219 1.535462 GCCATGCTTAGACGTGTTTGT 59.465 47.619 0.00 0.00 0.00 2.83
986 2221 1.535462 GTGCCATGCTTAGACGTGTTT 59.465 47.619 0.00 0.00 0.00 2.83
987 2222 1.156736 GTGCCATGCTTAGACGTGTT 58.843 50.000 0.00 0.00 0.00 3.32
990 2225 0.608130 TGAGTGCCATGCTTAGACGT 59.392 50.000 0.00 0.00 0.00 4.34
992 2227 3.338249 TCTTTGAGTGCCATGCTTAGAC 58.662 45.455 0.00 0.00 0.00 2.59
993 2228 3.701205 TCTTTGAGTGCCATGCTTAGA 57.299 42.857 0.00 0.00 0.00 2.10
994 2229 4.978083 ATTCTTTGAGTGCCATGCTTAG 57.022 40.909 0.00 0.00 0.00 2.18
995 2230 5.945784 AGTAATTCTTTGAGTGCCATGCTTA 59.054 36.000 0.00 0.00 0.00 3.09
1011 2267 3.118738 GGGTGACGGACATGAGTAATTCT 60.119 47.826 0.00 0.00 0.00 2.40
1824 3080 2.605607 TACTCCCTCCACCCGTCGA 61.606 63.158 0.00 0.00 0.00 4.20
1825 3081 2.044650 TACTCCCTCCACCCGTCG 60.045 66.667 0.00 0.00 0.00 5.12
1826 3082 2.413142 CGTACTCCCTCCACCCGTC 61.413 68.421 0.00 0.00 0.00 4.79
1827 3083 2.362120 CGTACTCCCTCCACCCGT 60.362 66.667 0.00 0.00 0.00 5.28
1828 3084 3.834799 GCGTACTCCCTCCACCCG 61.835 72.222 0.00 0.00 0.00 5.28
1829 3085 3.468140 GGCGTACTCCCTCCACCC 61.468 72.222 0.00 0.00 0.00 4.61
1830 3086 1.623542 AATGGCGTACTCCCTCCACC 61.624 60.000 0.00 0.00 0.00 4.61
1840 3096 1.523938 GCTCCCTCCAATGGCGTAC 60.524 63.158 0.00 0.00 0.00 3.67
1888 3144 1.215382 CGTGGAGGCGATGAACAGA 59.785 57.895 0.00 0.00 0.00 3.41
1944 3201 2.411547 GCCACAGTTCTCAAAATCGTCG 60.412 50.000 0.00 0.00 0.00 5.12
1988 3247 7.230108 CCTGCAGAAAATATACCAAGATCACAT 59.770 37.037 17.39 0.00 0.00 3.21
1990 3249 6.543831 ACCTGCAGAAAATATACCAAGATCAC 59.456 38.462 17.39 0.00 0.00 3.06
2006 3265 0.318441 CCTTCTCGTCACCTGCAGAA 59.682 55.000 17.39 0.00 0.00 3.02
2008 3267 0.534412 ATCCTTCTCGTCACCTGCAG 59.466 55.000 6.78 6.78 0.00 4.41
2046 3308 1.383799 CCAATGCCAGTCCTTCCCA 59.616 57.895 0.00 0.00 0.00 4.37
2171 3433 1.658686 GGTCAGCGATCTCACCTCGT 61.659 60.000 0.00 0.00 38.37 4.18
2271 3534 9.326413 GCAACTACACCATATTCAAAGTAGTAT 57.674 33.333 0.00 0.00 40.68 2.12
2272 3535 8.537016 AGCAACTACACCATATTCAAAGTAGTA 58.463 33.333 0.00 0.00 40.68 1.82
2273 3536 7.334421 CAGCAACTACACCATATTCAAAGTAGT 59.666 37.037 0.00 0.00 42.64 2.73
2274 3537 7.549134 TCAGCAACTACACCATATTCAAAGTAG 59.451 37.037 0.00 0.00 36.08 2.57
2330 3622 1.538512 GGCAAACGGAGGGAGTAAAAC 59.461 52.381 0.00 0.00 0.00 2.43
2338 3630 0.955919 GACTTGAGGCAAACGGAGGG 60.956 60.000 0.00 0.00 0.00 4.30
2342 3634 1.156736 ATTCGACTTGAGGCAAACGG 58.843 50.000 0.00 0.00 0.00 4.44
2343 3635 2.969443 AATTCGACTTGAGGCAAACG 57.031 45.000 0.00 0.00 0.00 3.60
2349 3665 6.821665 TCAAACCCTATAAATTCGACTTGAGG 59.178 38.462 0.00 0.00 0.00 3.86
2410 3743 8.645814 ATCTGTACCGTTAGATACATAATGGA 57.354 34.615 10.85 0.00 42.24 3.41
2420 3753 8.879759 CACAATAACAAATCTGTACCGTTAGAT 58.120 33.333 0.00 0.00 33.45 1.98
2426 3759 7.526608 ACATTCACAATAACAAATCTGTACCG 58.473 34.615 0.00 0.00 33.45 4.02
2461 3794 9.191479 TCCTGAAGTTTAACAAAGTTTATCCAA 57.809 29.630 0.00 0.00 34.32 3.53
2463 3796 9.678941 CTTCCTGAAGTTTAACAAAGTTTATCC 57.321 33.333 0.00 0.00 34.32 2.59
2480 3813 5.818136 TGTTTCAACTCAACTTCCTGAAG 57.182 39.130 5.37 5.37 43.79 3.02
2481 3814 6.183360 GGATTGTTTCAACTCAACTTCCTGAA 60.183 38.462 0.00 0.00 30.52 3.02
2482 3815 5.299279 GGATTGTTTCAACTCAACTTCCTGA 59.701 40.000 0.00 0.00 30.52 3.86
2483 3816 5.067674 TGGATTGTTTCAACTCAACTTCCTG 59.932 40.000 0.00 0.00 32.58 3.86
2484 3817 5.200483 TGGATTGTTTCAACTCAACTTCCT 58.800 37.500 0.00 0.00 32.58 3.36
2485 3818 5.514274 TGGATTGTTTCAACTCAACTTCC 57.486 39.130 0.00 0.00 32.26 3.46
2486 3819 5.403466 GCATGGATTGTTTCAACTCAACTTC 59.597 40.000 0.00 0.00 0.00 3.01
2487 3820 5.163426 TGCATGGATTGTTTCAACTCAACTT 60.163 36.000 0.00 0.00 0.00 2.66
2488 3821 4.341806 TGCATGGATTGTTTCAACTCAACT 59.658 37.500 0.00 0.00 0.00 3.16
2489 3822 4.619973 TGCATGGATTGTTTCAACTCAAC 58.380 39.130 0.00 0.00 0.00 3.18
2490 3823 4.933505 TGCATGGATTGTTTCAACTCAA 57.066 36.364 0.00 0.00 0.00 3.02
2491 3824 4.933505 TTGCATGGATTGTTTCAACTCA 57.066 36.364 0.00 0.00 0.00 3.41
2492 3825 5.291971 ACTTTGCATGGATTGTTTCAACTC 58.708 37.500 0.00 0.00 0.00 3.01
2493 3826 5.280654 ACTTTGCATGGATTGTTTCAACT 57.719 34.783 0.00 0.00 0.00 3.16
2494 3827 5.989551 AACTTTGCATGGATTGTTTCAAC 57.010 34.783 0.00 0.00 0.00 3.18
2495 3828 6.998968 AAAACTTTGCATGGATTGTTTCAA 57.001 29.167 14.79 0.00 0.00 2.69
2496 3829 6.998968 AAAAACTTTGCATGGATTGTTTCA 57.001 29.167 14.79 0.00 0.00 2.69
2518 3851 9.185680 GGGATGCTAGGAAATACTTTCTTTAAA 57.814 33.333 0.00 0.00 39.59 1.52
2519 3852 8.557450 AGGGATGCTAGGAAATACTTTCTTTAA 58.443 33.333 0.00 0.00 39.59 1.52
2520 3853 8.102484 AGGGATGCTAGGAAATACTTTCTTTA 57.898 34.615 0.00 0.00 39.59 1.85
2521 3854 6.974795 AGGGATGCTAGGAAATACTTTCTTT 58.025 36.000 0.00 0.00 39.59 2.52
2522 3855 6.582929 AGGGATGCTAGGAAATACTTTCTT 57.417 37.500 0.00 0.00 39.59 2.52
2523 3856 6.360618 CAAGGGATGCTAGGAAATACTTTCT 58.639 40.000 0.00 0.00 39.59 2.52
2524 3857 5.532779 CCAAGGGATGCTAGGAAATACTTTC 59.467 44.000 0.00 0.00 38.94 2.62
2525 3858 5.193728 TCCAAGGGATGCTAGGAAATACTTT 59.806 40.000 0.00 0.00 0.00 2.66
2526 3859 4.726825 TCCAAGGGATGCTAGGAAATACTT 59.273 41.667 0.00 0.00 0.00 2.24
2533 3866 0.839946 GCTTCCAAGGGATGCTAGGA 59.160 55.000 13.97 0.00 45.59 2.94
2537 3870 2.439156 GCGCTTCCAAGGGATGCT 60.439 61.111 17.60 0.00 46.46 3.79
2540 3873 2.092323 GTAAAAGCGCTTCCAAGGGAT 58.908 47.619 25.24 1.21 41.06 3.85
2553 3886 3.674753 TCACGTTAGCGGTTAGTAAAAGC 59.325 43.478 3.45 3.41 43.45 3.51
2561 3894 1.470285 GCCAGATCACGTTAGCGGTTA 60.470 52.381 3.45 0.00 43.45 2.85
2572 3905 1.953559 TTATGCGAAGGCCAGATCAC 58.046 50.000 5.01 0.00 38.85 3.06
2573 3906 2.708216 TTTATGCGAAGGCCAGATCA 57.292 45.000 5.01 0.00 38.85 2.92
2579 3912 3.518634 TCCAAAATTTATGCGAAGGCC 57.481 42.857 0.00 0.00 38.85 5.19
2612 3989 4.546570 CCCAAAACAAAAGAGACGGAATC 58.453 43.478 0.00 0.00 0.00 2.52
2616 3993 2.028876 ACCCCAAAACAAAAGAGACGG 58.971 47.619 0.00 0.00 0.00 4.79
2663 4040 4.275443 CCATTCCTTCAGCATTCTTCTAGC 59.725 45.833 0.00 0.00 0.00 3.42
2689 4066 1.137872 CTGCCCACTGGATGTCTCTAC 59.862 57.143 0.00 0.00 0.00 2.59
2690 4067 1.489481 CTGCCCACTGGATGTCTCTA 58.511 55.000 0.00 0.00 0.00 2.43
2706 4084 1.008079 GTGTGAGCCAGTTTGCTGC 60.008 57.895 0.00 0.00 42.95 5.25
2867 4251 0.518636 CAGCGACCTGACATTGTTGG 59.481 55.000 7.85 7.85 41.77 3.77
2956 4340 2.102252 CCTAGACTCATGTGCCCTTCTC 59.898 54.545 0.00 0.00 0.00 2.87
2957 4341 2.114616 CCTAGACTCATGTGCCCTTCT 58.885 52.381 0.00 0.00 0.00 2.85
2979 4363 7.001073 GTCAGAAAGGAAAGGGCTATTATCAT 58.999 38.462 0.00 0.00 0.00 2.45
3004 4389 0.171007 CAAGTAAGGCGCAACCATGG 59.829 55.000 11.19 11.19 43.14 3.66


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.